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- PDB-5djf: Structure of M. tuberculosis CysQ, a PAP phosphatase - ligand-fre... -

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Basic information

Entry
Database: PDB / ID: 5djf
TitleStructure of M. tuberculosis CysQ, a PAP phosphatase - ligand-free structure
Components3'-phosphoadenosine 5'-phosphate phosphatase
KeywordsHYDROLASE / CysQ / PAP phosphatase / apo-enzyme
Function / homology
Function and homology information


Sulfate assimilation / 3'(2'),5'-bisphosphate nucleotidase / 3'(2'),5'-bisphosphate nucleotidase activity / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / inositol monophosphate 1-phosphatase activity / sulfate assimilation / fructose-bisphosphatase ...Sulfate assimilation / 3'(2'),5'-bisphosphate nucleotidase / 3'(2'),5'-bisphosphate nucleotidase activity / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / inositol monophosphate 1-phosphatase activity / sulfate assimilation / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cobalt ion binding / manganese ion binding / magnesium ion binding / metal ion binding / plasma membrane
Similarity search - Function
Inositol monophosphatase, metal-binding site / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family
Similarity search - Domain/homology
3'-phosphoadenosine 5'-phosphate phosphatase / 3'-phosphoadenosine 5'-phosphate phosphatase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å
AuthorsErickson, A.I. / Fisher, A.J.
CitationJournal: Biochemistry / Year: 2015
Title: Crystal Structures of Mycobacterium tuberculosis CysQ, with Substrate and Products Bound.
Authors: Erickson, A.I. / Sarsam, R.D. / Fisher, A.J.
History
DepositionSep 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3'-phosphoadenosine 5'-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9544
Polymers30,7471
Non-polymers2073
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-13 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.320, 57.900, 101.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3'-phosphoadenosine 5'-phosphate phosphatase / CysQ / PAP phosphatase / 3'(2') / 5'-bisphosphate nucleotidase / 5-bisphosphonucleoside 3'(2')- ...CysQ / PAP phosphatase / 3'(2') / 5'-bisphosphate nucleotidase / 5-bisphosphonucleoside 3'(2')-phosphohydrolase / D-fructose-1 / 6-bisphosphate 1-phosphohydrolase / DPNPase / Fructose-1 / 6-bisphosphatase / FBPase / Inositol-1-monophosphatase / IMPase / Inositol-1-phosphatase


Mass: 30746.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cysQ, MT2189 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WKJ0, UniProt: P9WKJ1*PLUS, 3'(2'),5'-bisphosphate nucleotidase, fructose-bisphosphatase, inositol-phosphate phosphatase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.27 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: 24% PEG1500, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2013
RadiationMonochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 1.7→38.203 Å / Num. all: 26208 / Num. obs: 26208 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.19 % / Biso Wilson estimate: 15.25 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.46
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 2.41 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.6 / % possible all: 92.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASERphasing
XSCALEJuly 4, 2012data scaling
XDSMarch 30, 2013data scaling
XDSdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→38.203 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 18.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 1326 5.06 %Random selection
Rwork0.162 ---
obs0.1639 26208 97.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→38.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 13 295 2322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122087
X-RAY DIFFRACTIONf_angle_d1.4112850
X-RAY DIFFRACTIONf_dihedral_angle_d12.613754
X-RAY DIFFRACTIONf_chiral_restr0.085318
X-RAY DIFFRACTIONf_plane_restr0.006377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7002-1.76820.28941170.22082650X-RAY DIFFRACTION94
1.7682-1.84870.23571460.19272698X-RAY DIFFRACTION97
1.8487-1.94620.21751420.17232736X-RAY DIFFRACTION98
1.9462-2.06810.22361450.16612736X-RAY DIFFRACTION97
2.0681-2.22780.17491420.16192761X-RAY DIFFRACTION98
2.2278-2.45190.22091490.16172765X-RAY DIFFRACTION98
2.4519-2.80660.1971710.15762780X-RAY DIFFRACTION98
2.8066-3.53560.17431650.15122811X-RAY DIFFRACTION98
3.5356-38.21250.19071490.15312945X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.7844-0.6585-1.1182.1167-0.99012.16110.0553-0.46890.48570.29220.03960.58130.0442-0.2831-0.09920.12410.01370.02280.249400.2382-14.142129.323619.9405
21.48050.48170.15792.40720.06810.6919-0.0342-0.012-0.0139-0.07060.0619-0.08660.01420.058-0.02780.04190.0030.0010.07520.0010.03867.671132.595321.0695
31.12650.2069-1.17070.9443-0.25151.7863-0.04390.21180.0795-0.18720.0910.0119-0.0865-0.0883-0.04430.1158-0.0172-0.01840.11530.02140.08454.415638.35484.5151
40.2120.3286-0.4360.5689-0.55911.4345-0.0201-0.0372-0.0377-0.0433-0.0462-0.07450.01650.1520.06520.13330.0050.00910.12030.00340.11913.261530.67322.8479
52.6222-2.1952-3.94544.54612.80817.2472-0.02520.2338-0.0474-0.25890.0192-0.24050.47550.03220.03230.2014-0.01830.04390.1521-0.00350.122413.47328.1114-9.3387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid -18:17)
2X-RAY DIFFRACTION2(chain A and resid 18:123)
3X-RAY DIFFRACTION3(chain A and resid 124:164)
4X-RAY DIFFRACTION4(chain A and resid 165:249)
5X-RAY DIFFRACTION5(chain A and resid 250:267)

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